You guys are overlooking the Gemini. It has as much cargo space as a mule, is faster, holds more fuel, takes less fuel/LR, has more flux dissipation, more efficient shields, PD drones, 2 medium ballistic slots, (which don't have to be PD because of it's drones,) and finally, a flight deck.
True, it has less ordinance points and armor, but that is pretty much it. By itself the mule might be a little better, but the flight decks certainly make the gemini a better ship to have in your fleet. So the mule is not unbalanced.
Oh, and the tarsus has a burn drive, which is one of the best hull mods for a freighter to have I think.